Drugs for cancer therapy belong to different categories of chemical substances. The cellular targets for the therapeutic efficacy are often not unambiguously identified. Here, we describe the process of ribosome biogenesis as a target of a large variety of chemotherapeutic drugs. We determined the inhibitory concentration of 36 chemotherapeutic drugs for transcription and processing of ribosomal RNA by in vivo labeling experiments. Inhibitory drug concentrations were correlated to the loss of nucleolar integrity. The synergism of drugs inhibiting ribosomal RNA synthesis at different levels was studied. Drugs inhibited ribosomal RNA synthesis either at the level of (i) rRNA transcription (e.g. oxaliplatin, doxorubicin, mitoxantrone, methotrexate), (ii) early rRNA processing (e.g. camptothecin, flavopiridol, roscovitine), or (iii) late rRNA processing (e.g. 5-fluorouracil, MG-132, homoharringtonine). Blockage of rRNA transcription or early rRNA processing steps caused nucleolar disintegration, whereas blockage of late rRNA processing steps left the nucleolus intact. Flavopiridol and 5-fluorouracil showed a strong synergism for inhibition of rRNA processing. We conclude that inhibition of ribosome biogenesis by chemotherapeutic drugs potentially may contribute to the efficacy of therapeutic regimens.Chemotherapeutic drugs (hereinafter drugs) are used for the treatment of neoplastic diseases for more than 50 years. The mode of action and specifically the therapeutic relevant targets of many drugs, however, are often less defined. Recent studies revealed that some drugs like 5-fluorouracil (5-FU), 4 which were first assumed to interfere with DNA metabolism actually act mainly on RNA metabolism (1-9). In fact an increasing number of analyses identifies RNA metabolism as an important target of cancer drugs.In a hallmark study, Rubbi and Milner (10) showed that accumulation of the tumor suppressor p53 in UV-or drug-damaged cells occurs only if nucleolar functions are affected. Local, severe UV irradiation of the nucleoplasm could not stabilize p53 accumulation. In contrast, UV damage in the nucleolus induced a strong p53 response suggesting that the major sensor controlling the stability and degradation of p53 is located in the nucleolus, the place of ribosome biogenesis.The stability of the p53 protein is controlled by the ubiquitin ligase Mdm2, which targets p53 to the proteasome for degradation. Strikingly, several ribosomal proteins, including L5, L11, L23, and S7 proteins can bind and inactivate . Conditional knockdown of these ribosomal protein genes prevents Mdm2 inactivation and p53 stabilization in 5-FU-treated cells (15), consistent with the assumption that destruction of nucleolar functions by 5-FU inhibits ribosome biogenesis and results in liberation of ribosomal proteins followed by Mdm2 inactivation and p53 stabilization. The inhibition of rRNA transcription by knockout of the gene for the RNA polymerase I (Pol I) transcription factor TIF-1A (16), by blockage of the transcription factor UBF after microin...

RNA synthesis and decay rates determine the steady-state levels of cellular RNAs. Metabolic tagging of newly transcribed RNA by 4-thiouridine (4sU) can reveal the relative contributions of RNA synthesis and decay rates. The kinetics of RNA processing, however, had so far remained unresolved. Here, we show that ultrashort 4sU-tagging not only provides snapshot pictures of eukaryotic gene expression but, when combined with progressive 4sU-tagging and RNA-seq, reveals global RNA processing kinetics at nucleotide resolution. Using this method, we identified classes of rapidly and slowly spliced/degraded introns. Interestingly, each class of splicing kinetics was characterized by a distinct association with intron length, gene length, and splice site strength. For a large group of introns, we also observed long lasting retention in the primary transcript, but efficient secondary splicing or degradation at later time points. Finally, we show that processing of most, but not all small nucleolar (sno)RNA-containing introns is remarkably inefficient with the majority of introns being spliced and degraded rather than processed into mature snoRNAs. In summary, our study yields unparalleled insights into the kinetics of RNA processing and provides the tools to study molecular mechanisms of RNA processing and their contribution to the regulation of gene expression.

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DNA is constantly exposed to endogenous and exogenous damage. Various types of DNA repair counteract highly toxic DNA double-strand breaks (DSBs) to maintain genome stability. Recent findings suggest that the human DNA damage response (DDR) utilizes small RNA species, which are produced as long non-coding (nc)RNA precursors and promote recognition of DSBs. However, regulatory principles that control production of such transcripts remain largely elusive. Here we show that the Abelson tyrosine kinase c-Abl/ABL1 causes formation of RNA polymerase II (RNAPII) foci, predominantly phosphorylated at carboxy-terminal domain (CTD) residue Tyr1, at DSBs. CTD Tyr1-phosphorylated RNAPII (CTD Y1P) synthetizes strand-specific, damage-responsive transcripts (DARTs), which trigger formation of double-stranded (ds)RNA intermediates via DNA–RNA hybrid intermediates to promote recruitment of p53-binding protein 1 (53BP1) and Mediator of DNA damage checkpoint 1 (MDC1) to endogenous DSBs. Interference with transcription, c-Abl activity, DNA–RNA hybrid formation or dsRNA processing impairs CTD Y1P foci formation, attenuates DART synthesis and delays recruitment of DDR factors and DSB signalling. Collectively, our data provide novel insight in RNA-dependent DDR by coupling DSB-induced c-Abl activity on RNAPII to generate DARTs for consequent DSB recognition.